Britain and Russia are on a collision course over Alexander Litvinenko's death after a coroner said an inquest would be held early next year and would hear allegations that the spy was murdered by the Russian state.

The coroner, Sir Robert Owen, said he regretted that it had taken so long to hold an inquest into Litvinenko's death nearly six years ago. "There will be no further delay," he said. "It's manifestly in the interests of his widow, Marina, and his son, Anatoly … of other interested persons and in the wider public interest, that [this] is brought to a conclusion."

Litvinenko, a dissident and former Russian intelligence officer, died in November 2006 after ingesting polonium-210, a rare radioactive isotope. The Crown Prosecution Service has accused Andrei Lugovoi, a former KGB agent, of putting polonium in Litvinenko's tea during a meeting at London's Millennium Hotel. A second former KGB agent, Dmitry Kovtun, was also present at the meeting.

At Thursday's hearing it emerged that the British authorities had formally accused Kovtun of Litvinenko's murder. Both accused men have denied involvement and claim they are victims themselves. In 2007, the Kremlin flatly refused a British request to extradite Lugovoi, leading to a row with Moscow and the tit-for-tat expulsion of Russian and British diplomats. Lugovoi is now a deputy in Russia's Duma.

The Foreign Office had previously tried to limit the scope of the inquest, fearing further diplomatic fallout. But Owen said he endorsed a ruling by his predecessor in the case, Dr Andrew Reid, that there should be an "open and fearless" investigation. It would examine the theory that "Russian state agents" killed Litvinenko. A previously secret report by the Metropolitan police into the Litvinenko case, including vital forensic evidence, would be circulated early next month to "interested parties", he said.

Ben Emmerson QC, acting for Marina Litvinenko, said she wanted the inquest to examine the "alleged criminal role of the Russian state". It should determine "whether her husband's killing was a targeted assassination of a British citizen committed by agents of a foreign state in the sovereign territory of the United Kingdom". If proved, this would be "an act of state-sponsored nuclear terrorism on the streets of London", he said.

Marina Litvinenko said she was pleased there would finally be a full inquest. It is likely to take place in early 2013.

"We can't get a real trial and we can't get any justice. This [the inquest] will maybe give us some answers," she said.

Alex Goldfarb, Litvinenko's close friend, said it was significant that the CPS had enough evidence to charge both Lugovoi and Kovtun. "We have a group. We have a pre-organised plot. There are superiors," he said.

"The inquest will hopefully uncover what really happened," Goldfarb added. "We and many others think this was a political murder perpetrated by the Russian state, possibly on the personal orders of Vladimir Putin. But there is no evidence for that. It's circumstantial. We don't know what is in the police file. We don't have the autopsy report. We don't know what the [British secret] services have. We know they were lurking in the background."

The coroner said Scotland Yard had investigated whether Litvinenko, who fled from Russia to Britain in 2000, had been in contact with MI5 and MI6. He said the Yard's conclusions would remain secret at the request of the government.

He ruled that the home secretary could be an "interested party" in the case. Other interested parties include Marina Litvinenko and her son; Litvinenko's first family, who live in Russia; the oligarch and Kremlin critic Boris Berezovsky; Lugovoi, Kovtun, the CPS and the Met.

Louise Christian, Marina Litvinenko's solicitor, said she was optimistic that the judge's ruling on MI5 and MI6 could be challenged at a later stage and evidence from the intelligence services eventually revealed. Asked what the Met's report might contain, she said: "I think it will confirm the forensic trail that links Lugovoi and Kovtun to the eventual murder. There was [polonium] contamination on three separate occasions."

She added: "We are extremely positive. We believe that British justice will be done."

Ever since Litvinenko's murder, Russia has waged a concerted propaganda campaign to blame his killing on Berezovsky, Litvinenko's patron and the Kremlin's No 1 enemy. Lugovoi's spectacular political rise – he is a deputy with the ultra-nationalist Liberal Democrat party – has fuelled speculation that he enjoys support from the top of Russian power. Lugovoi is likely to give evidence at the inquest via a video link from Moscow. He has hired a legal team.

Despite his repeated protestations of innocence, British detectives are convinced the forensic trail leads back to Moscow. They say only a state or state organisation would have been in position to get hold of polonium, an extremely rare substance. US diplomatic cables reveal that Kovtun allegedly left traces of polonium across nothern Germany in the hours before he flew to London for his fateful meeting with Litvinenko. German police were said to have discovered polonium on Kovtun's rented BMW and the sofa where he slept.

Privately, British diplomats admit that the inquest is likely to cause a fresh rift with Moscow and further infuriate Putin. David Cameron has been trying to improve bilateral relations, which were frosty under Labour. The prime minister visited Moscow last year, and Putin came to London in August to watch the Olympics. Russia's president remains furious at the UK's refusal to extradite Berezovsky and other exiles including the Chechen separatist leader Akhmad Zakayev, who attended Thursday's hearing.

The next pre-inquest hearings will take place on 2 November and 13-14 December. The court has launched a new website with information about the case.